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Phytophagous mites in the genus Brevipalpus (Tenuipalpidae) can be major pests, causing direct damage to their host plants or vectoring viruses. However, a phylogeny-based classification to understand their evolution and predict their…
Interacting, self-propelled particles such as epithelial cells can dynamically self-organize into complex multicellular patterns, which are challenging to classify without a priori information. Classically, different phases and phase…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
The Rosids is one of the largest groups of flowering plants, with 140 families and ~70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
We present a novel approach for taxonomic analysis of chloroplast genomes in angiosperms using the Pan-genome Research Toolkit (PGR-TK). Comparative plots generated by PGR-TK across diverse angiosperm genera reveal a wide range of…
Principal components (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples sampled from a given environment. However, a classical application of…
Chloroplast sequences from the Lamiales order were analyzed using the Pangenome Research Toolkit (PGR-TK). Overall, most genera and families exhibited a high degree of sequence uniformity. However, at the genus level, Utricularia,…
The aim of Galactic archaeology is to recover the history of our Galaxy through the information encoded in stars. An unprobed assumption of this field is that the chemical composition of a star is an immutable marker of the gas from which…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small…
Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
Computational topologists recently developed a method, called persistent homology to analyze data presented in terms of similarity or dissimilarity. Indeed, persistent homology studies the evolution of topological features in terms of a…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
We propose a novel framework for reconstructing the chronology of genetic regulation using causal inference based on Pearl's theory. The approach proceeds in three main stages: causal discovery, causal inference, and chronology…
Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…